Initialize repo

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$
+^data-raw$
+^R-raw$
+^README\.Rmd$
+^README-.*\.png$
+^\.github$

.github/.gitignore

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+*.html

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

DESCRIPTION

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+Package: multinichenetr
+Type: Package
+Title: Cell-Cell Communication analysis for scRNAseq data with complex multi-sample multi-group designs 
+Version: 0.1.0
+Author: person("Robin", "Browaeys", email = "[email protected]",
+  role = c("aut", "cre"))
+Maintainer: Robin Browaeys <[email protected]>
+Description: This package allows you the investigate intercellular communication from a computational perspective. 
+    It is an extension of the NicheNet framework (https://github.com/saeyslab/nichenetr) to better suit scRNAseq datasets with complex designs.
+    These datasets can contain multiple samples (e.g. patients) over different groups of interest (e.g. disease subtypes). 
+    With MultiNicheNet, you can now better analyze the differences in cell-cell signaling between the different groups of interest.
+    MultiNicheNet will give a you a list of the ligand-receptor interactions that are most strongly differentially expressed between patients of the different groups, and also most active in the different groups as given by the NicheNet ligand activity.
+License: GPL-3
+Encoding: UTF-8
+LazyData: true
+URL: https://github.com/browaeysrobin/multinichenetr
+BugReports: https://github.com/browaeysrobin/multinichenetr/issues
+Depends: R (>= 3.4.0)
+Imports: 
+    Seurat,
+    dplyr,
+    circlize,
+    patchwork,
+    ggplot2,
+    tibble,
+    tidyr,
+    purrr,
+    ComplexHeatmap,
+    stringr,
+    generics,
+    grid,
+    Nebulosa
+Remotes: 
+  github::saeyslab/nichenetr
+RoxygenNote: 7.1.1

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(combine_sender_receiver_de)
+export(combine_sender_receiver_info_ic)
+export(fix_frq_df)
+export(generate_prioritization_tables)
+export(get_avg_frac_exprs_abund)
+export(get_ligand_activities_targets_DEgenes)
+export(get_muscat_exprs_avg)
+export(get_muscat_exprs_frac)
+export(make_circos_group_comparison)
+export(make_featureplot)
+export(make_group_lfc_exprs_activity_plot)
+export(make_ligand_activity_plots)
+export(make_ligand_activity_target_plot)
+export(make_ligand_receptor_nebulosa_feature_plot)
+export(make_ligand_receptor_violin_plot)
+export(make_nebulosa)
+export(make_sample_lr_prod_activity_plots)
+export(make_sample_lr_prod_plots)
+export(make_sample_target_plots)
+export(make_sample_target_plots_reversed)
+export(make_target_nebulosa_feature_plot)
+export(make_target_violin_plot)
+export(ms_mg_nichenet_analysis)
+export(ms_mg_nichenet_analysis_combined)
+export(ms_mg_nichenet_analysis_separate)
+export(perform_muscat_de_analysis)
+export(process_info_to_ic)
+import(Seurat)
+import(dplyr)
+import(muscat)
+importFrom(purrr,map)

R-raw/add_data.R

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+library(Seurat)
+library(tidyverse)
+
+# add visium
+seurat_obj = readRDS("C:/Users/rbrowaey/work/Research/NicheNet/current_projects/CRC_NicheNet/data/seurat_obj_lite_hnscc.rds")
+usethis::use_data(seurat_obj,overwrite = T, compress = "bzip2")
+
+
+usethis::use_package("Seurat")
+usethis::use_package("dplyr")
+usethis::use_package("ggplot2")
+usethis::use_package("circlize")
+usethis::use_package("patchwork")
+
+usethis::use_package("Scater")
+usethis::use_package("Muscat")
+usethis::use_package("tibble")
+usethis::use_package("tidyr")
+usethis::use_package("purrr")
+usethis::use_package("ComplexHeatmap")
+
+usethis::use_package("circlize")
+usethis::use_package("stringr")
+usethis::use_package("generics")
+usethis::use_package("ComplexHeatmap")
+usethis::use_package("grid")
+usethis::use_package("Nebulosa")
+
+
+

R/data.R

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+## description of data
+
+#' Seurat object containing scRNAseq data (subsampled)
+#'
+#' Seurat object containing scRNAseq data (subsampled). Source of the data: Puram et al., Cell 2017: “Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer.”. This example data was downsampled (features and cells).
+#'
+#' @format An object of class Seurat
+#'
+"seurat_obj"